As to my understanding, In the configuration example AN84868, the configuration data are entirely stored at the FX3 before the vender command is sent. Some FPGA have a small volumn of configruation data and therefore can be stored. The configruation data of the FPGA I use achieves 2.7M Bytes. Is the ram of FX3 large enough to hold the data? If not, is there any solution?

The configuration data is not stored in the FX3 RAM. The configuration data of the FPGA is sent through the host application to the FX3 through USB and then to the FPGA. This will not limit your bitstream size as it is stored in the PC and not in the FX3 RAM.